Cylindrical2dNodesOnlyMesh.cpp

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*/
 
#include <map>
#include "Cylindrical2dNodesOnlyMesh.hpp"
 
Cylindrical2dNodesOnlyMesh::Cylindrical2dNodesOnlyMesh(double width)
        : NodesOnlyMesh<2>(),
          mWidth(width)
{
    assert(width > 0.0);
}
 
void Cylindrical2dNodesOnlyMesh::SetUpBoxCollection(double cutOffLength, c_vector<double, 2*2> domainSize, int numLocalRows, c_vector<bool,2> isDimPeriodic)
{
    // Ensure that the width is a multiple of cut-off length
    if (fmod( mWidth,cutOffLength ) > 1e-14)
    {
        EXCEPTION("The periodic width must be a multiple of cut off length.");
    }
    else if (mWidth/cutOffLength == 2.0)
    {
        // A width of two boxes gives different simulation results as some connections are considered twice.
        EXCEPTION( "The periodic domain width cannot be 2*CutOffLength." );
    }
 
    // We force the domain to the periodic width
    domainSize[0] = 0;
    domainSize[1] = mWidth;
 
    // Forcde the periodicity to periodic only in x
    isDimPeriodic  = zero_vector<bool>(2);
    isDimPeriodic[0]  = true;
 
 
    NodesOnlyMesh<2>::SetUpBoxCollection(cutOffLength, domainSize, PETSC_DECIDE, isDimPeriodic);    // Only difference is that this "true" makes the boxes periodic.
 
    this->AddNodesToBoxes();
}
 
double Cylindrical2dNodesOnlyMesh::GetWidth(const unsigned& rDimension) const
{
    double width = 0.0;
    assert(rDimension==0 || rDimension==1);
    if (rDimension==0)
    {
        width = mWidth;
    }
    else
    {
        width = MutableMesh<2,2>::GetWidth(rDimension);
    }
    return width;
}
 
 
void Cylindrical2dNodesOnlyMesh::SetNode(unsigned nodeIndex, ChastePoint<2> point, bool concreteMove)
{
    // concreteMove should always be false for NodesOnlyMesh as no elements to check
    assert(!concreteMove);
 
    double x_coord = point.rGetLocation()[0];
 
    // Perform a periodic movement if necessary
    if (x_coord >= mWidth)
    {
        // Move point to the left
        point.SetCoordinate(0, x_coord - mWidth);
    }
    else if (x_coord < 0.0)
    {
        double new_x_coord = x_coord + mWidth;
        double fudge_factor = 1e-14;
        // This is to ensure that the position is never equal to mWidth, which would be outside the box domain.
        // This is due to the fact that mWidth-1e-16=mWidth
        if (new_x_coord > mWidth-fudge_factor)
        {
            new_x_coord = mWidth-fudge_factor;
        }
        point.SetCoordinate(0, new_x_coord);
    }
 
    // Update the node's location
    this->GetNode(nodeIndex)->SetPoint(point);
}
 
unsigned Cylindrical2dNodesOnlyMesh::AddNode(Node<2>* pNewNode)
{
    // Call method on parent class
    unsigned node_index = NodesOnlyMesh<2>::AddNode(pNewNode);
 
    // If necessary move it to be back on the cylinder
    ChastePoint<2> new_node_point = pNewNode->GetPoint();
    SetNode(node_index, new_node_point);
 
    return node_index;
 
}
 
c_vector<double, 2> Cylindrical2dNodesOnlyMesh::GetVectorFromAtoB(const c_vector<double, 2>& rLocation1, const c_vector<double, 2>& rLocation2)
{
    c_vector<double, 2> vector = rLocation2 - rLocation1;
    vector[0] = fmod(vector[0], mWidth);
 
    /*
     * Handle the cylindrical condition here: if the points are more
     * than halfway around the cylinder apart, measure the other way.
     */
    if (vector[0] > 0.5*mWidth)
    {
        vector[0] -= mWidth;
    }
    else if (vector[0] < -0.5*mWidth)
    {
        vector[0] += mWidth;
    }
    return vector;
}
 
// Refresh mesh -> Check and then move if outside box
void Cylindrical2dNodesOnlyMesh::RefreshMesh()
{
 
    // Check if the x values are in the domain, if not, get the fmod and relocate.
    unsigned num_nodes = mNodes.size();
    for (unsigned i=0; i<num_nodes; i++)
    {
        double& x_location = (mNodes[i]->rGetModifiableLocation())[0];
        if (x_location < 0.0)
        {
            x_location = fmod(x_location, mWidth) + mWidth;
        }
        else if (x_location >= mWidth)
        {
            x_location = fmod(x_location, mWidth);
        }
    }
 
    // Now run the base class method
    NodesOnlyMesh<2>::RefreshMesh();
}
 
// Serialization for Boost >= 1.36
#include "SerializationExportWrapperForCpp.hpp"
CHASTE_CLASS_EXPORT(Cylindrical2dNodesOnlyMesh)